Changes

   vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --max_r2 0.2 --min_avg_dp 2 --out_map chr1.r0.2.map

   vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --max_r2 0.2 --min_avg_dp 2 --out_map chr1.r0.2.map

* polymutt2: taking a VCF and the map file generated by vcf2map

* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)

  polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf

  polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf

  polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --best_path

  polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --best_path